ID_engine: ID_engine

In Ulises-Rosas/boldminer: Wrapper for BOLD API and DNA barcode auditing

Description

ID_engine finds best matches between a query sequence and a database of BOLD by using BLASTn-based algorithms. Arguments of this function are 'query' and 'db'. The first one are query sequences and the second one are one of avilable databases in BOLD:

- 'COX1'

- 'COX1_SPECIES'

- 'COX1_SPECIES_PUBLIC'

- 'COX1_L640bp'

Usage

ID_engine(query, db, make_blast = TRUE, quiet = FALSE)

Arguments

query	query
db	db
make_blast	make_blast
quiet	if TRUE, suppress running messages while running

Value

species ID

Examples

## Not run: 
fasta_file <- system.file("sequences.fa", package = "boldminer")
out <- boldminer::ID_engine(query = fasta_file, db = "COX1_SPECIES")


## End(Not run)

Ulises-Rosas/boldminer documentation built on Dec. 18, 2019, 2:53 a.m.